[BioC] GenomeGraphs question

[Iain Gallagher]

Dear List

I am plotting some snps using GenomeGraphs to show genomic context. I have a simple question: how do I change the size of the plotting character?

# SCRIPT BEGINS

require(biomaRt) # get and load the library
require(GenomeGraphs) 

# get the snps we need info on
snps <- c('rs136617760', 'rs42494357', 'rs110465273', 'rs42494342',  'rs109809949', 'rs134449285', 'rs137562332', 'rs132841890')

# set up the database we need to query
snpmart <- useMart('snp', dataset = 'btaurus_snp')

# we want to get the snp id, allele, chromosome position and chromosome
# in biomaRt attributes are what you want, filters are what you're using to query the db
# there's load of info available; use listAttributes(snpmart) to see what you can get back
# and listFilters(snpmart) to see what you can put in as a query

snpInfo <- getBM(attributes = c('refsnp_id', 'allele', 'chrom_start', 'chr_name'), filters = 'snp_filter', values = snps, mart = snpmart)

# plot these using GenomeGraphs
# subset out the chromosome 13 snps
thirteenSnps <- subset(snpInfo, snpInfo$chr_name == 13)

# make pretend 'intensity values' for later
ints <- seq(1,6) # could replace with 1/log10p perhaps!
names(ints) <- thirteenSnps$refsnp_id
ints <- as.matrix(ints)

# set up mart
cowmart <- useMart('ensembl', dataset = 'btaurus_gene_ensembl')

# make a plot of the genes on bovine chromosome 13 around the SNPs Mairead found on chromosome 13
ideogram <- makeIdeogram(chromosome = 13)

plusStrand <- makeGeneRegion(chromosome = 13, start = min(thirteenSnps$chrom_start)-5e5, end = min(thirteenSnps$chrom_start)+5e5, strand = "+", biomart = cowmart)

minStrand <- makeGeneRegion( chromosome = 13, start = min(thirteenSnps$chrom_start)-5e5, end = min(thirteenSnps$chrom_start)+5e5, strand = "-", biomart = cowmart)

genomeAxis <- makeGenomeAxis(add53 = TRUE, add35 = TRUE)

snpPlot <- makeGenericArray(intensity = ints, probeStart = thirteenSnps$chrom_start,  dp = DisplayPars(color="darkred", type="point", cex = 2))

gdPlot(list(makeTitle('Chromosome 13'), a = ideogram, b = plusStrand, c = genomeAxis, d = minStrand, e = snpPlot), labelCex = 2, labelRot = 0)

# SCRIPT ENDS

I would like to make the dots representing the snps larger. I tried e.g.

dp = DisplayPars(cex = 2) and dp = DisplayPars(size = 2) in the snpPlot definition without success and I can't work out the answer from the documentation.

Incidentally I'm aware that the above script is perhaps abusing makeGenericArray - it works for me. If anyone has a more 'proper' way of doing this then that would be educational as well.

Best

Iain

> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=C                LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GenomeGraphs_1.14.0 biomaRt_2.10.0      ggplot2_0.9.0      

loaded via a namespace (and not attached):
 [1] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.1       MASS_7.3-16       
 [5] memoise_0.1        munsell_0.3        plyr_1.7.1         proto_0.3-9.2     
 [9] RColorBrewer_1.0-5 RCurl_1.9-5        reshape2_1.2.1     scales_0.1.0      
[13] stringr_0.6        tools_2.14.1       XML_3.9-2         
>